NetCDFPeakFinding {TargetSearch} | R Documentation |
This function reads a netcdf chromatogram file, finds the apex intensities and returns a list containing the retention time and the intensity matrices.
NetCDFPeakFinding(cdfFile, massRange = NULL, Window = 15, IntThreshold = 10, pp.method = "ppc", baseline = FALSE, baseline.opts = NULL)
cdfFile |
A character string naming a netcdf file. |
massRange |
A two component numeric vector with the scan mass range to extract
or |
Window |
The window used by peak picking method. The number of points actually used
is |
IntThreshold |
Apex intensities lower than this value will be removed from the RI files. |
pp.method |
The pick picking method to be used. Options are |
baseline |
Logical. Should baseline correction be performed? |
baseline.opts |
A list of options passed to |
.
The function expects the following NetCDF variables: intensity_values
,
mass_values
, scan_index
, point_count
and scan_acquisition_time
.
Otherwise, an error will be displayed.
The massRange
parameter is a numeric vector with two components: lower
and higher masses. All masses in that range will be extracted. Note that it is
not possible to extract a discontinuous mass range. It also can be NULL
,
in which case the mass range will be determined by scanning the cdf file.
There are two peak picking algorithms that can be used. The "smoothing"
method
smooths the m/z curves and then looks for a change of sign of the intensity difference
between two consecutive points. The "ppc"
uses a sliding window and looks
for the local maxima. This method is based on R-package ppc
.
A three component list.
Time |
The retention time vector. |
Peaks |
The intensity matrix. Rows are the retention times and columns are masses. The first column is the lower mass value and the last one is the higher mass. |
massRange |
The mass range. |
Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig
require(TargetSearchData) CDFpath <- file.path(find.package("TargetSearchData"), "gc-ms-data") CDFfiles <- dir(CDFpath, pattern = ".cdf$", full.names = TRUE) CDFfiles # extrac peaks of first chromatogram peaks.1 <- NetCDFPeakFinding(CDFfiles[1], massRange = c(85, 320), Window = 15, IntThreshold = 10, pp.method = "smoothing") # scan acquisition times head(peaks.1$Time) # peaks in matrix form. first column is mass 85, last one is mass 320. head(peaks.1$Peaks)